MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b3831 b4069 b3752 b2297 b2458 b2779 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b3945 b1602 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.464051 (mmol/gDw/h)
  Minimum Production Rate : 0.006093 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.059157
  EX_o2_e : 287.277648
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.011714
  EX_pi_e : 0.453719
  EX_so4_e : 0.116857
  EX_k_e : 0.090580
  EX_mg2_e : 0.004026
  EX_cl_e : 0.002415
  EX_ca2_e : 0.002415
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992547
  EX_h2o_e : 551.226151
  EX_co2_e : 37.576230
  EX_fum_e : 0.696623
  EX_ac_e : 0.270164
  Auxiliary production reaction : 0.006093
  EX_3hpp_e : 0.006093
  DM_mththf_c : 0.000208
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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